A Stream of Consciousness
by MacGateFan
Summary: Tentative title. Written for another SGA Santa Community on LJ. Prompt: WeirSheppard where John is evil and bad and possibly hurts Elizabeth. Slight spoilers for Lifeboat SG1 and The Long Goodbye.
1. What happened to John Sheppard?

Title: A Stream of Consciousness  
Rating: PG13  
Author: MacGateFan  
Disclaimers: All characters and the series are property of people who aren't me.  
Notes: This was written for another SGA Secret Santa on LJ.

* * *

Elizabeth found John on the east pier, arms resting on the railing. If he knew she was there, he gave no indication. Two days ago, he and Rodney had set out into one of the unexplored sections of Atlantis and found trouble.

Go figure!

No matter where John Sheppard went, trouble followed. The pair found an Ancient lab with technology scattered all over the place. John's hand accidentally brushed against one of them and he immediately fell unconscious.

He woke up nearly three hours later, not remembering anything about what happened. Carson had released him with instructions to go directly to his quarters, but Elizabeth knew the man standing before her.

Before Elizabeth could say anything to him, John had turned around to face her. He immediately grabbed her wrist and squeezed hard. He didn't even flinch as she cried out in pain.

Elizabeth looked into his eyes, but saw nothing familiar within them, only hatred and anger.

"John?"

"I'm leaving and you're coming with me."

"What?" she asked. "What are you talking about? John, you're hurting me!"

In response, John smacked her across the face. "Shut up!" he growled, pulling her back inside.

Elizabeth was too scared to respond to him. What was going on? What could have happened to make him act in such a way?

As John stopped in his quarters, rummaging around for various items, Elizabeth quickly tapped her earpiece and kept it in her hand. She sighed with relief when she saw that he didn't notice what she was doing.

"Where are we going, John?"

"We're just going to dial and go. Once we get there, you'll meet your fate."

Elizabeth didn't know how to respond to that. She just silently prayed that someone was listening in on their conversation.

* * *

_"Where are we going, John?"_

_"We're just going to dial and go. Once we get there, you'll meet your fate._"

Chuck glanced over at Radek. From the look of it, they were the only ones to hear the conversation going on.

_"Why are you doing this?"_

_"You know why! I've told you a thousand times, your people will not be the cause of more deaths! It's your fault the Wraith were created. It's your fault our world was culled by them. You will pay, Serenity!"_

"Who's Serenity?" Chuck mouthed to the Czech.

Radek shook his head, but he would find out. First, however, he needed to inform Major Lorne, Ronon, Teyla, and Rodney of the situation.

* * *

Rodney stood with Zelenka and Chuck in the control room while Lorne, Teyla, and Ronon stood to the left of the Stargate, waiting for John to appear with Elizabeth. They were each armed, Lorne and Teyla with a Wraith stunner and Ronon with his own weapon.

_"Major,"_ Rodney's voice filtered through his earpiece, _"they should be coming around the corner in a few minutes. Their life signs are close together so it's possible you may have to shoot them both."_

"Got it," Lorne replied, clearly not happy about having to shoot either of his bosses.

He didn't even get a chance to blink because the minute they stepped into view, Ronon fired. Amazingly he only hit John. Elizabeth stared at them in shock for a few minutes, and then shouted, "We need a medical team here now!"

* * *

Carson sighed as he finished his exam of John. He hated having to tell them that there didn't seem to be anything physically wrong with the man. True, they had to wait for the blood work...

"I've got it!" Rodney exclaimed, rushing into the infirmary.

"What is it, Rodney?" Elizabeth asked. Carson noted that her face seemed a little pale and her voice shaky. Not doubt still in shock over what happened.

Rodney presented her the laptop in his hands. "The Ancients were housing a consciousness in the device he touched."

"Bloody hell," Carson muttered. "Not again."

He heard the voices talking about his host as he carefully cracked opened his eyes. Glancing to his left was the one known as Carson Beckett, the physician.

To his right was Major Lorne and the man had a semi automatic weapon in the holster strapped to his leg. He could tell his host was surprised that he wasn't in restraints.

Without a word, he seamlessly got up from the bed, grabbed the weapon, smacking the Major in the mouth with his elbow and pointed the gun at Elizabeth Weir.

"Mynar, put the gun down," Rodney said. "We are not Ancients, we're peaceful explorers from another galaxy and we've been studying Atlantis and its technology. If you can read Colonel Sheppard's thoughts, you know this!"

Mynar glared at Rodney, albeit a little shocked the man knew his name, and shook his head. "No! I am ignoring his thoughts right now. I don't care about him and I don't care about any of you! I just want my revenge!"

He sensed someone coming behind him and before anyone could react, he fired the weapon. Ronon grabbed the gun and knocked him unconscious.

"Elizabeth!" Carson exclaimed rushing to her still body on the floor.

"Carson," she whispered in a scared voice.

He gently moved her hand from her stomach, watching in stunned silence as the dark red blood spread across her shirt. "Dear, God!"

Carson finally snapped out of his haze, barking out orders right and left. Rodney watched in horror as the medical team lifted Elizabeth and placed her on a gurney. The blood that remained on the floor made him feel weak at the knees.

"Rodney," a voice said softly. He looked up at Teyla and let her guide him to a chair. "Will you be all right?" she asked.

He nodded slowly. "I-I think so. I should probably figure out a way to help Sheppard since I can't… I can't do anything for Elizabeth right now."

"I am certain Colonel Sheppard would be grateful. We must learn more of this Mynar. Is the name of his people listed somewhere? Perhaps I can go to the mainland and ask about them."

"I didn't see a name yet, but I'll let you know when I do," he replied, looking up at Ronon. "Sheppard?"

"Major Lorne thought it would be best to keep him in restraints for now. Doc seemed to agree."

Rodney sighed. He did not relish the sight of his friend in restraints so; instead, he decided to grab Radek and head back to the lab where they first encountered that annoying piece of technology. "Call me when Carson's finished with Elizabeth or Mynar," he had a faint note of disgust when the name was said, "wakes up."

"We will be sure to, Rodney," Teyla told him.


	2. Mynar & Serenity

A Stream of Consciousness  
Part 2  
Author: MacGateFan  
Disclaimers in Part 1

* * *

Rodney looked up from the text he was reading and sighed. He could definitely use Elizabeth's help with the translation. "Anything?" he asked Zelenka.

"I cannot translate any of this. Maybe you could have a look?"

"As much as I hate to admit it," Rodney said, rubbing his eyes, "I'm having problems translating as well. Let's go over what we know and then we'll go from there."

Zelenka nodded. "Yes, that is good idea. Mynar is from a race of people who were allies with the Ancients at one time."

"But their people were culled by the Wraith," Rodney continued, "and they blamed the Ancients for it. Mynar mentioned Serenity. Let's see if we can't find her in the database."

The pair was silent as Rodney began a search for the name. After ten long minutes, the console beeped and two pages of information spilled onto the screen.

Rodney scanned the information. "According to this, Serenity was one of the Ancient's leading scientists in the creation of the Wraith. Just like nearly everything they experiment with, it went haywire and they purposely let the Wraith loose on that planet."

"My God," Zelenka said. "It looks like they didn't expect them to be so smart and create ships and weapons."

"Wonderful. And no wonder Mynar is hell bent on killing Elizabeth, he thinks she's Serenity. Look at the image of her."

Zelenka muttered a curse in Czech. Elizabeth and Serenity could be twins. "Okay, so this tells us why this is happening, but how can we stop this and get Colonel Sheppard back?"

"I'm afraid we'll have to wait until Elizabeth is able to look over this text," Rodney replied.

* * *

Dr. Francesca Brown glanced at the EEG screen. She was not happy about the current readings. In fact, they were beginning to scare her.

She looked up when Carson came into view. Her boss looked decidedly exhausted, which no doubt came from miraculously saving the life of Elizabeth Weir.

According to Suzy, they nearly lost her twice. If Colonel Sheppard was still aware of everything going on, he was going to need one hell of a therapy session after the entity was removed.

"Franny, Love, how's the Colonel?"

"Not well, Carson. Do you remember reading the file on Dr. Jackson from a few years ago?"

Carson thought a moment. "Aye that I do. He had the consciousness of 12 people in his mind. They nearly lost him..." He trailed off. "Are you saying that we may lose Colonel Sheppard?"

"I'm afraid so. If you take a look here," she said, pointing to the EEG screen, "you can see the two separate brain patterns. The top one is the Colonel's as compared to ones he's had in the past and the bottom is Mynar."

"Bottom line is we need to get Mynar out of him before he has complete control of Colonel Sheppard and we lose our friend forever."

Franny nodded. She took a deep breath and asked, "How's Dr. Weir?"

"She's stable for right now. The bullet hit her lower abdomen and nicked an artery. But we were able to remove it and we've repaired the artery. We're just lucky this happened in here."

"Lucky," Franny muttered.

Carson smiled warily. "I should report this to Rodney. After all, he's in charge at the moment."

* * *

John could feel Mynar's pain and anger and he felt it consuming him. Mynar's mind had taken control of the pilot and he could do nothing but watch as Mynar attacked Elizabeth. He tried to scream, but the sound went nowhere. He would have rather pointed the gun at himself than shoot Elizabeth. God, was she all right? He didn't know and Mynar wasn't telling him.

"Get out of my mind!" John cried out.

Mynar laughed. "Once my revenge is complete, you may have your body back. I know how you feel about Serenity. What would you do if I told you she was dead? That you killed her."

"No!" John replied. "I didn't have anything to do that!"

"You may keep telling you that if you wish. If you'll excuse me, I have things to do."

John had no choice but to slip away…

* * *

Elizabeth woke up to blazing pain in her side. She looked groggily to her left and saw John restrained in the bed next to her. He didn't appear to be conscious, though.

For the moment, she was grateful for that. She didn't think she could handle seeing those cold eyes. True, she knew in her heart it was Mynar, but seeing the expression and utter hatred in John Sheppard's eyes was something she wasn't ready to face again.

"Elizabeth?"

She blinked a few times to see Carson's head swimming above her. Elizabeth's throat was dry and Carson noticed this as he reached for the cup of ice. "Take it easy, Love," he said.

Elizabeth savored the cool wetness as it went down her throat. "Is he all right?" she asked, looking over at John again.

"For the moment," Carson replied. "We have him sedate while Rodney figures out how to remove Mynar's consciousness from the Colonel's mind."

Her heart began racing as she recalled Dr. Frasier's file on Daniel's condition a few years back. "Oh God, Carson!" she gasped.

"No doubt you're thinking of Dr. Jackson's situation. We're aware of that and we're not going to let anything happen to him, I promise."

Elizabeth was a little surprised to see Carson inject something to her IV. _When had he gotten that?_ She wondered as she slowly slipped into the darkness.


	3. Elizabeth Wakes Up

A Stream of Consciousness  
Part 3  
Author: MacGateFan  
Disclaimers in Part 1

* * *

Rodney was tapping away at his laptop when Elizabeth regained consciousness. She began assessing the pain. _Not too bad… wait, don't move so much and its fine,_ she thought to herself.

"Elizabeth," Rodney said with a smile. "I'll be right back; I'm going to get Carson."

Rodney knew Carson would stab him with pointy needles if he didn't get the physician. His exact words were, 'Do not let her touch your computer until I've checked her over or so help me!'

"How are you feeling, Elizabeth?" Carson asked.

"The pain isn't so bad right now," she replied. "It only hurts if I move so I've decided to keep still for the moment."

He smiled. "Good. I was a wee bit worried earlier because you lost a fair amount of blood."

"Where are Teyla and Ronon?"

Rodney spoke up; telling her about Mynar's people and the Ancient translations then mentioned that the pair had gone to the Mainland to gather any information they could regarding them.

"Let me see the laptop, Rodney," she said. "We need to figure out a way to help John."

Carson sighed. He didn't like this, but it was probably their only chance to save their friend. "Just take it easy, Elizabeth, and let me know if you start feeling more pain."

"I will, Carson."

Ronon and Elizabeth arrived about 20 minutes later. "Any luck?" Rodney asked.

"None," Teyla replied. "My people remember an enemy who were angry at the Ancients for the Wraith, but they had never met them nor know of where they came from."

Ronon watched Elizabeth as she intently poured over the contents on the computer. "What about you guys?"

Elizabeth looked up at them. "According to this, Mynar's people were known as the Cerise. They lived on a planet about five light years from here and they met the Ancients two years before the Wraith came into existence.

"After the Cerise were culled, the Ancients offered the small remaining group sanctuary in Atlantis. Only a handful remained, including Mynar. When he learned where the Wraith came from, they attempted to destroy Atlantis. Everyone but Mynar was killed and his consciousness was some how transferred into the device that John touched."

Rodney eyed her curiously. "It doesn't say how he was transferred?"

She shook her head. "No, just that he was. That's where I left off."

Carson chose that moment to walk over. "Elizabeth, Love, I really think you should rest. You've been sitting up all day and even though you won't admit it, I can tell you're in pain."

"Carson, I do not plan on stopping the translation until I find out how to save John. Didn't you say that we may very well lose him completely if Mynar remains?" He gave a curt nod. "Then until Mynar is gone, I will not rest!"

"Very well, but the moment you've finished, I'm going to sedate you for at least 24 hours!"

Elizabeth was just about finished translating the lab data when she started feeling dizzy. Rodney immediately sensed something wrong and leapt from his chair. "Are you all right?" he asked, as Teyla rushed to find Carson.

"I'm fine, Rodney," she replied. He could tell she was lying because she looked deathly pale. "And I may have found a way to remove Mynar."

"How?"

She glanced up at Ronon and replied, "We need the device John touched. According to the instructions Serenity left, there are settings on it that will extract a consciousness."

Elizabeth took a deep breath. "That's how they stopped Mynar's attack to begin with. Their intention was to remove him from his body and bring him back to Cerise. Only the device didn't work and Mynar's body died."

"Okay," Rodney said, "I'm sure I can figure out the settings. What's to say we won't pull Sheppard's consciousness along with Mynar's? Did Serenity mention that?"

"I'm afraid she didn't, Rodney."

"Elizabeth!" Carson exclaimed, rushing over. He could tell that she was in pain, but masking it well. Along with the fact that her eyes were now bright with a fever. "It's time to rest, Love."

She looked up at him dizzily and, although she wanted to be awake to make sure she wasn't going to lose John, she was exhausted. "Rodney, you should be able to read the settings in her findings. Just help him."

"Don't worry about a thing," he replied.

"Franny," Carson said as the other physician appeared, please check on Colonel Sheppard. I'll be there for the transfer, but I'd like you to be there as well."

"Of course, Carson."

Carson helped Elizabeth get settled on the bed. "Are you comfortable?"

"As comfortable as I can be. I'm sorry I over did it, Carson, but even though I'm in pain, I'll be all right. John has helped me as well as everyone in Atlantis a hundred times over, I just figured it was about time someone helped him."

He smiled. "Aye. You just rest now and I'll repeat what Rodney said, don't worry! Pretty soon you'll have Colonel Sheppard begging us to be put back on duty."

"I can't wait," Elizabeth whispered as the medication Carson gave her went into effect.

* * *

Rodney looked up at Carson and Franny, a look of pure terror on his face. "I just… I mean, I don't know if this is really going to work."

"Just take a deep breath, Rodney," Carson said. "Let Colonel Sheppard know what's going on. He knows how hard we're trying to save him."

Rodney nodded, explaining to John what was going on as he changed the last setting on the device. He could feel Teyla, Ronon and Lorne's presence behind him and that gave him strength. "Here goes," he whispered, touching John's hand to the device.

A few minutes later, the device blinked and let off a series of beeps, and then all was quiet. "Did it work?" Ronon asked.

Franny looked over at the EEG monitors. "I only see one brainwave pattern, but it's very weak." She continued to stare at the pattern, trying to see anything in it that would tell her whose it was.

"Franny?"

She sighed in relief. "Carson, its Colonel Sheppard's."

"Oh thank God!" Rodney exclaimed. His legs absolutely felt like jello. "I think I'm gonna pass out!"

Ronon and Teyla rushed to his side as he listed to the left. "Rodney?" Teyla said.

"I-I'm fine. Just… I'm fine!"

"All the same get some rest," Carson told them all.

When they were gone, he turned to see Franny checking John's vitals. "How's he doing, Love?"

"He should be all right, but he's exhausted beyond belief. Carson, it's a good thing we got Mynar out of his mind when we did. Another hour or so and we would have lost him completely."

* * *

John felt truly and utterly alone. Mynar told him that his friends weren't coming to save him. They hated him for what he did to Elizabeth. He still couldn't believe he had killed her. He saw the weapon in his own hands. Saw the look in her eyes as he pulled the trigger.

He really didn't feel like going back to reality, but he knew he would have to face it sooner or later. John sighed. _Might as well get this over with,_ he thought…

"He's coming to, Carson!" a familiar voice said. At the moment, he couldn't figure out who that was.

John tried opening his eyes a crack, but shut them when bright light seeped through. "It's all right, Colonel, I've turned the lights down."

Another familiar voice, this one with an accent. "Carson?"

"Aye, Colonel." John opened his eyes to see the physician smiling at him. "We're very happy to have you back."

John stared at him in confusion. That couldn't be right. Mynar had said they didn't want anything to do with him. Why were they happy to have him back? No, don't feel sorry for yourself, remember the most important person to ask about!

"Elizabeth?"

Carson moved to the right so John could see the bed next to him. "She's fine, Colonel and resting right now."

"No thanks to you… Hey, ouch! I mean, Mynar."

John looked up at Rodney. "I shot her."

"No," Teyla responded, "you did not shoot Elizabeth, Mynar did."

That couldn't be right. He could see it happen over and over in his mind. He shot her. He nearly killed her. It was his fault. All his fault!

"Colonel!" Carson exclaimed as his heart raced. He called for a sedative and continued to try and calm the man down. He wasn't succeeding so he called Teyla over as the nurse arrived with a syringe.

Teyla gently took John's face into her hands and looked into his eyes. "John, listen to me. John! What happened was not your fault, do you understand me? Elizabeth is safe and she will be all right, I promise."

John nodded, but he still seemed unconvinced. "John, have I ever lied to you?" Teyla asked.

"No…" he whispered, drifting into darkness.


	4. John Wakes Up

A Stream of Consciousness  
Part 4  
Author: MacGateFan  
Disclaimers in Part 1

* * *

Rodney sat in Elizabeth's office staring into space. He couldn't believe two of the first people he trusted the most had been fighting for their lives nearly a day ago. Now he was stuck as temporary leader of Atlantis and he wasn't all that happy about it.

When Colonel Caldwell arrived tomorrow, he didn't think he would like it either. In fact, he knew the commander of the Daedalus would leap at the chance to be in control.

That wasn't fair. Caldwell could be a pain in the ass, but he has helped saved them in the past despite the whole possessed by a Goa'uld thing.

Right now the thing he feared the most was the weekly check in with Earth. What were they going to say when they learned the Atlantis base leader and chief military officer were both lying in the infirmary?

Rodney's thoughts went back to his friends. When Mynar shot Elizabeth, a look of shock and terror was seen briefly on John's face. And all that blood. She was lucky to be alive.

He shuddered, upset about how morbid his thoughts had just become. He was about to call Carson to check on their status, when Chuck knocked on the door. "Dr. McKay, time for the weekly check in."

"Be right there," he managed to reply. How, he didn't know.

* * *

"You're making excellent progress, Love," Carson told Elizabeth. Her wound had healed nicely and she would be in her quarters later that evening. "The only thing I'm concerned about is that you don't seem interested in speaking with Colonel Sheppard."

Elizabeth nodded slowly, but didn't reply. "I realize this is difficult for you, but you have to understand it wasn't him."

She nodded again. "I know, Carson. It's just... Mynar didn't make it easy for me. I know looking like Serenity didn't help either. John... His eyes were so cold. I keep telling myself it wasn't him, but my eyes don't want to believe my mind."

"Aye, that's understandable," Carson replied.

Elizabeth swallowed around the lump in her throat. "It'll just take some time."

"Normally, I would agree with you, Dr. Weir, but we don't have much time right now."

"Why? What is it?"

"Colonel Sheppard isn't sleeping well and has been unable to keep any food down. Everytime he thinks about what happens, he becomes naseous or has the most terrifying dreams one could only imagine."

Elizabeth's eyes widened. "Is it that bad?"

"He's seem to have lost any will to live. Kate and I are afraid that if you can't help him to see past it and that you don't believe he did the things Mynar did, we're going to lose him."

Carson hated telling Elizabeth that. In fact, he felt that he was blaming her for the Colonel's condition. Kate had insisted it would be all right, but he wasn't so sure. The utter look of despair on Elizabeth's face made him realize what a mistake that one sentence was.

He was a little surprised, though, when she took a deep breath and looked him straight in the eyes, determination on her face. "I'll talk to him, Carson."

"All right, Love. He's awake right now, albeit a mite quiet. Even Rodney's hasn't been able to get a rise out of him."

She nodded as Carson helped her to sit up. The pain in her side had significantly lessened and once again she found herself thanking the SGC for sending such a competent medical staff. It was a little difficult walking the few feet to John's bed and she was nearly exhausted as Carson helped her sit.

Rodney looked at her and smiled. She returned the smile, and then took a deep breath, taking John's hand in hers. She noticed him tense, but he never turned to face her, only kept looking at Rodney.

"Sheppard," he said, "Elizabeth would like to talk to you."

Elizabeth had to strain to hear his response. "She doesn't want to talk to me. She shouldn't even be anywhere near me. I almost killed her, Rodney. I'm not safe to be around anymore."

"Okay!" Rodney exclaimed, "That's enough!"

Before Carson could even move, the astrophysicist had John by arm and was yanking at him to sit up. "I am so sick of you whining and crying about this! You didn't do anything wrong! Elizabeth is right there, alive and she doesn't blame you! No one does so get your head out of your ass and get over it!"

For the first time, John turned to face Elizabeth. She looked up at him and gave him a smile. "Rodney's right, you know. I don't blame you. It's true what Mynar did through you scared me, but I know you would never hurt me, John."

"I…"

Carson watched the scene in complete shock. He was even more shocked at John's lack of speech. "Colonel?"

"I'm sorry," he gasped out. "I guess I really don't have an excuse for my behavior. I just want to get back to work."

"You're going to need to talk to Dr. Heightmeyer before you're back on duty, Son," the physician replied.

He nodded, clearly not happy about it. "Can I talk to Elizabeth alone?" he asked in a more subdued voice.

"Aye that you can. Come on, Rodney."

When the pair was out of earshot, John had finally settled back onto the bed. He looked over at Elizabeth and could tell she looked about as exhausted as he felt. He knew they would have to talk about this sooner or later.

John took a deep breath and began. "I was fine for awhile after Carson released me from the infirmary. When I got to my quarters, I realized something wasn't right. I needed air so I headed to the balcony.

"By the time you arrived, Mynar had taken over. I tried to fight him as he grabbed you. When he hit you, I screamed. When he shot you, I nearly died. He blamed me. Said it was my fault and for some reason I believed him. I don't know if he made me believe it or if I really thought I had done it."

Elizabeth nodded in sympathy. She remembered what it had felt like to have another consciousness in control and John had to endure it twice.

"I'm sorry I've been ignoring you. I shouldn't have done that. I know you could never hurt like that and you would kill anyone who tried. I guess it's a little difficult to do when it's just a consciousness in your mind."

"A little," John admitted, closing his eyes.

Elizabeth noticed a slight wince. "Headache?" she asked. At his nod, she gingerly got up, telling him she was getting Carson.

"Is everything all right, Love?" Carson wanted to know after he had gotten her and John both settled.

"It will be, Carson," she replied. She eyed him curiously. "And I thought I was getting out of here tonight."

"Tomorrow, I promise."

Elizabeth decided not to argue with the man as he turned and headed to his office. Besides, she could keep an eye on John Sheppard from where she was. She had a feeling Carson did this purposely, and she was grateful. Besides, technically she couldn't go back to work after Kate cleared her as well.

"Elizabeth."

"John, you're supposed to be sleeping."

"I know."

"Then why are talking to me?"

"Because."

Elizabeth smiled as she drifted off to sleep. That was as good a reason as any.


End file.
